discoal: flexible coalescent simulations with selection

BioRxiv : the Preprint Server for Biology
Andrew D Kern, Daniel R Schrider

Abstract

Here we describe discoal, a coalescent simulator able to generate population samples that include selective sweeps in a feature-rich, flexible manner. discoal can perform simulations conditioning on the fixation of an allele due to drift or either hard or soft selective sweeps, even those occurring a large genetic distance away from the simulated locus. discoal can simulate sweeps with recurrent mutation to the adaptive allele, recombination, and gene conversion, under non-equilibrium demographic histories and without specifying an allele frequency trajectory in advance. Availability and Implementation: Availability and implementation: discoal is implemented in the C programming language. Source code is freely available on GitHub (https://github.com/kern-lab/discoal_multipop) under a GNU General Public License.

Related Concepts

Alleles
Genes
Laboratory Procedures
Recombination, Genetic
Fixation - Action
Gene Mutation
Simulation
Population Group
Locus
R Programming Language

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